Brett Knight was arraigned Friday in Central Islip. He also pleaded not guilty to aggravated harassment.
Prosecutors allege Knight fired 11 times through a window of Ross Reisner's East Setuaket home on September 24, killing him.
He's being held without bail. His next court date is Oct. 16.
The 50-year-old Reisner was a fixture in Eastern Suffolk County's equestrian community. Knight was believed to be a former tenant.
Reisner and his longtime domestic partner, Kevin Murray, who was grazed by one of the bullets, filed a harassment complaint against Knight last month.
The shooting spurred a nationwide search for Knight, who had purchased a motorcycle and was said to be traveling throughout the country. Knight was considered armed, volatile and extremely dangerous.